Hi Rick,
Thank you very much for the clear explanation of the order of align and volreg blocks and the relevance of skull stripping to surface-based analyses. As for the alignment issues, I am still having no luck.
I ran my preprocessing script with 3 different align_epi_anat.py variations which are below and I get the exact same alignment, which is poor in every case. I also thought maybe I just had a weird participant, so I did this on two different individuals with the same result. The resulting (lack of) coverage of my epis on my surface model are identical for each variation of align_epi_anat.py (I tried to attach photos but it wouldn't work). Any ideas how I can fix this? Its worth mentioning that this is happening with approximately half of my participants (n=9 out of 19), so it is a big problem for me at the moment. Please let me know if I can provide you with additional information to help you diagnosis the problem.
Thanks,
Kara
# ================================= defaults ==================================
align_epi_anat.py -epi2anat -anat struct+orig \
-save_skullstrip -suffix _al_junk \
-epi pb01.$subj.r01.tshift+orig -epi_base 2 \
-epi_strip 3dAutomask \
-volreg off -tshift off
# ================================= big move + partial coverage ==================================
align_epi_anat.py -epi2anat -anat struct+orig -big_move -partial_coverage \
-save_skullstrip -suffix _al_junk \
-epi pb01.$subj.r01.tshift+orig -epi_base 2 \
-epi_strip 3dAutomask \
-volreg off -tshift off
# ================================= lpc+ZZ + giant move ==================================
align_epi_anat.py -epi2anat -anat struct+orig \
-save_skullstrip -suffix _al_junk \
-epi pb01.$subj.r01.tshift+orig -epi_base 2 \
-epi_strip 3dAutomask \
-cost lpc+ZZ -giant_move \
-volreg off -tshift off
